def main():
options = parse_options()
exe = options.executable
inputdf = options.input
include = options.include_regexp
exclude = options.exclude_regexp
tag = options.tag
verbose = options.verbose
submit = options.submit
datasets = dataset.build_all_datasets_from_dir_or_file(inputdf)
datasets = utils.filterWithRegexp(
datasets, include, lambda _: _.name) if include else datasets
datasets = utils.excludeWithRegexp(
datasets, exclude, lambda _: _.name) if exclude else datasets
for dset in datasets:
if not get_filelist(dset.name):
print "# skipping (missing filelist) {0}".format(dset.name)
continue
script = get_batch_script(dset, options)
if not script:
if verbose:
print "skipping (do-not-overwrite) {0}".format(dset.name)
continue
cmd = "sbatch %s" % script
if verbose: print cmd
if submit:
out = utils.getCommandOutput(cmd)
if verbose: print out['stdout']
if not submit:
print "This was a dry run; use '--submit' to actually submit the jobs"
def main():
options = parse_options()
exe = options.executable
inputdf = options.input
include = options.include_regexp
exclude = options.exclude_regexp
tag = options.tag
verbose = options.verbose
submit = options.submit
datasets = dataset.build_all_datasets_from_dir_or_file(inputdf)
datasets = utils.filterWithRegexp (datasets, include, lambda _: _.name) if include else datasets
datasets = utils.excludeWithRegexp(datasets, exclude, lambda _: _.name) if exclude else datasets
for dset in datasets :
if not get_filelist(dset.name):
print "# skipping (missing filelist) {0}".format(dset.name)
continue
script = get_batch_script(dset, options)
if not script:
if verbose : print "skipping (do-not-overwrite) {0}".format(dset.name)
continue
cmd = "sbatch %s" % script
if verbose : print cmd
if submit :
out = utils.getCommandOutput(cmd)
if verbose : print out['stdout']
if not submit : print "This was a dry run; use '--submit' to actually submit the jobs"
def main():
options = parse_options()
inputdf = options.input
outdir = options.output_dir
regexp = options.sample_regexp
exclude = options.exclude_regexp
tag = options.tag
verbose = options.verbose
debug = options.debug
utils.mkdirIfNeeded(outdir)
if debug: dataset.Dataset.verbose_parsing = True
datasets = dataset.build_all_datasets_from_dir_or_file(inputdf)
datasets = utils.filterWithRegexp(datasets, regexp,
lambda _: _.name) if regexp else datasets
datasets = utils.excludeWithRegexp(
datasets, exclude, lambda _: _.name) if exclude else datasets
counter = {'fail': 0, 'pass': 0}
for d in datasets:
outcome = 'pass' if d.build_filelist(gpatlas_dir(d, tag), outdir,
verbose) else 'fail'
counter[outcome] += 1
if verbose:
print "created %d filelists (%d failures)" % (counter['pass'],
counter['fail'])
def main():
options = parse_options()
inputdf = options.input
outdir = options.output_dir
regexp = options.sample_regexp
exclude = options.exclude_regexp
tag = options.tag
verbose = options.verbose
debug = options.debug
utils.mkdirIfNeeded(outdir)
if debug : dataset.Dataset.verbose_parsing = True
datasets = dataset.build_all_datasets_from_dir_or_file(inputdf)
datasets = utils.filterWithRegexp (datasets, regexp, lambda _: _.name) if regexp else datasets
datasets = utils.excludeWithRegexp(datasets, exclude, lambda _: _.name) if exclude else datasets
counter = {'fail':0, 'pass':0}
for d in datasets:
outcome = 'pass' if d.build_filelist(gpatlas_dir(d, tag), outdir, verbose) else 'fail'
counter[outcome] += 1
if verbose:
print "created %d filelists (%d failures)" % (counter['pass'], counter['fail'])
